David Jimenez-Morales

Check my preprints from bioRxiv and medRxiv

2024 - MoTrPAC Study Group, Lead Analysts & MoTrPAC Study Group

Temporal dynamics of the multi-omic response to endurance exercise training

Nature. Volume 629, pages 174–183 (2024). Featured on the cover. doi: 10.1038/s41586-023-06877-w

2024 - David Amar, Nicole R. Gay, David Jimenez-Morales, Pierre M. Jean Beltran, Megan E. Ramaker, Archana Natarajan Raja, Bingqing Zhao, Yifei Sun, Shruti Marwaha, David A. Gaul, Steven G. Hershman, Alexis Ferrasse, Ashley Xia, Ian Lanza, Facundo M. Fernández, Stephen B. Montgomery, Andrea L. Hevener, Euan A. Ashley, Martin J. Walsh, Lauren M. Sparks, Charles F. Burant, R. Scott Rector, John Thyfault, Matthew T. Wheeler, Bret H. Goodpaster, Paul M. Coen, Simon Schenk, Sue C. Bodine, Malene E. Lindholm, the MoTrPAC Study Group

The mitochondrial multi-omic response to exercise training across rat tissues

Cell Metabolism. May 02, 2024. doi: 10.1016/j.cmet.2023.12.021

2024 - Gina M. Many, James A. Sanford, Tyler J. Sagendorf, Zhenxin Hou, Pasquale Nigro, Katie L. Whytock, David Amar, Tiziana Caputo, Nicole R. Gay, David A. Gaul, Michael F. Hirshman, David Jimenez-Morales, Malene E. Lindholm, Michael J. Muehlbauer, Maria Vamvini, Bryan C. Bergman, Facundo M. Fernández, Laurie J. Goodyear, Andrea L. Hevener, Eric A. Ortlund, Lauren M. Sparks, Ashley Xia, Joshua N. Adkins, Sue C. Bodine, The MoTrPAC Study Group

Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue

Nature Metabolism. 2024. Epub 2024 May 1. doi: 10.1038/s42255-023-00959-9

2024 - Adriana Steinbach, Varun Bhadkamkar, David Jimenez-Morales, Erica Stevenson, Gwendolyn M. Jang, Nevan J. Krogan, Danielle L. Swaney, and Shaeri Mukherjee

Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila

Molecular Biology of the Cell. 2024 Mar 1;35(3):ar27. doi: 10.1091/mbc.E23-06-0260

2023 - Zeynep Cakir, Samuel J Lord, Yuan Zhou, Gwendolyn M Jang, Benjamin J Polacco, Manon Eckhardt, David Jimenez-Morales, Billy W Newton, Adam L Orr, Jeffrey R Johnson, Alexandre da Cruz, R Dyche Mullins, Nevan J Krogan, Robert W Mahley, Danielle L Swaney

Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP

Molecular & Cellular Proteomics. 2023 May;22(5):100541. Epub 2023 Apr 4. doi: 10.1016/j.mcpro.2023.100541.

2023 - Kristoffer E. Leon, Mir M. Khalid, Ryan A. Flynn, Krystal A. Fontaine, Thong T. Nguyen, G. Renuka Kumar, Camille R. Simoneau, Sakshi Tomar, David Jimenez-Morales, Mariah Dunlap, Julia Kaye, Priya S. Shah, Steven Finkbeiner, Nevan J. Krogan, Carolyn Bertozzi, Jan E. Carette, Melanie Ott

Nuclear accumulation of host transcripts during Zika Virus Infection

PLoS Pathog. 2023 Jan 5;19(1):e1011070. doi: 10.1371/journal.ppat.1011070.

2022 - SH Lee, X Liu, D Jimenez-Morales, PF Rinaudo

Murine blastocysts generated by in vitro fertilization show increased Warburg metabolism and altered lactate production

Elife. 2022 Sep 15;11:e79153. doi: 10.7554/eLife.79153.

2022 - VN Parikh, AG Ioannidis, D Jimenez-Morales ,... , EA Ashley

Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy

Nature Communications. 2022 13 (1), 1-10. doi: 10.1038/s41467-022-32397-8.

2022 - Gabriel Mitchell, Melanie R Silvis, Kelsey C Talkington, Jonathan M Budzik, Claire E Dodd, Justin M Paluba, Erika A Oki, Kristine L Trotta, Daniel J Licht, David Jimenez-Morales, Seemay Chou, Paul B Savage, Carol A Gross, Michael A Marletta, Jeffery S Cox

Ceragenins and Antimicrobial Peptides Kill Bacteria through Distinct Mechanisms

mBio. 2022 Jan 25;e0272621. doi: 10.1128/mbio.02726-21.

2021 - Malene E Lindholm, David Jimenez-Morales, Han Zhu, Kinya Seo, David Amar, Chunli Zhao, Archana Raja, Roshni Madhvani, Sarah Abramowitz, Cedric Espenel, Shirley Sutton, Colleen Caleshu, Gerald J Berry, Kara S Motonaga, Kyla Dunn, Julia Platt, Euan A Ashley, Matthew T Wheeler

Mono- and Biallelic Protein-Truncating Variants in Alpha-Actinin 2 Cause Cardiomyopathy Through Distinct Mechanisms

Circ Genom Precis Med. 2021 Nov 22. doi: 10.1161/CIRCGEN.121.003419

2021 - Danielle L. Swaney, Dana J. Ramms, Zhiyong Wang, Jisoo Park, Yusuke Goto, Margaret Soucheray, Neil Bhola, Kyumin Kim, Fan Zheng, Yan Zeng, Michael McGregor, Kari A. Herrington, Rachel O’Keefe, Nan Jin, Nathan K. VanLandingham, Helene Foussard, John Von Dollen, Mehdi Bouhaddou, David Jimenez-Morales, Kirsten Obernier, Jason F. Kreisberg, Minkyu Kim, Daniel E. Johnson, Natalia Jura, Jennifer R. Grandis, J. Silvio Gutkind, Trey Ideker, Nevan J. Krogan

A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity

Science. Oct 1, 2021. doi: 10.1126/science.abf2911

2021 - Laura Martin-Sancho, Shashank Tripathi, Ariel Rodriguez-Frandsen, Lars Pache, Maite Sanchez-Aparicio, Michael J. McGregor, Kelsey M. Haas, Danielle L. Swaney, Thong T. Nguyen, Joao I. Mamede, Christopher Churas, Dexter Pratt, Sara B. Rosenthal, Laura Riva, Courtney Nguyen, Nish Beltran-Raygoza, Stephen Soonthornvacharin, Guojun Wang, David Jimenez-Morales, Paul D. De Jesus, Hong M. Moulton, David A. Stein, Max W. Chang, Chris Benner, Trey Ideker, Randy A. Albrecht, Judd F. Hultquist, Nevan J. Krogan, Adolfo García-Sastre & Sumit K. Chanda

Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy

Nature Microbiology. Sept 23, 2021. doi: 10.1038/s41564-021-00964-2

2021 - Esther Paulo, Yun Zhang, Ruchi Masand, Tony L. Huynh, Youngho Seo, Danielle L. Swaney, Margaret Soucheray, Erica Stevenson, David Jimenez-Morales, Nevan J. Krogan, Biao Wang

Brown adipocyte ATF4 activation improves thermoregulation and systemic metabolism

Cell Reports. Vol 36, Issue 12, 109742, Sept 21, 2021. doi: 10.1016/j.celrep.2021.109742

2021 - COVID-19 Host Genetics Initiative

Mapping the human genetic architecture of COVID-19

Nature. 2021 Jul 8. doi: 10.1038/s41586-021-03767-x

2021 - Nikoleta G Tsvetanova, Michelle Trester-Zedlitz, Billy W Newton, Grace E Peng, Jeffrey R Johnson, David Jimenez-Morales, Andrew P Kurland, Nevan J Krogan, Mark von Zastrow

Endosomal cAMP production broadly impacts the cellular phosphoproteome

J Biol Chem. 2021 Jun 21;100907. doi: 10.1016/j.jbc.2021.100907

2021 - Aaron J. Wilk, Madeline J. Lee, Bei Wei, Benjamin Parks, Ruoxi Pi, Giovanny J. Martínez-Colón, Thanmayi Ranganath, Nancy Q. Zhao, Shalina Taylor, Winston Becker, Stanford COVID-19 Biobank, David Jimenez-Morales, Andra L. Blomkalns, Ruth O’Hara, Euan A. Ashley, Kari C. Nadeau, Samuel Yang, Susan Holmes, Marlene Rabinovitch, Angela J. Rogers, William J. Greenleaf, Catherine A. Blish

Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19

J Exp Med. (2021) 218 (8): e20210582. doi: 10.1084/jem.20210582

2020 - The Molecular Transducers of Physical Activity Consortium

Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise

Cell. Volume 181, Issue 7, P1464-1474, June 25, 2020. doi: 10.1016/j.cell.2020.06.004

2020 - Jonathan M Budzik, Danielle L Swaney, David Jimenez-Morales, Jeffrey R Johnson, Nicholas E Garelis, Teresa Repasy, Allison W Roberts, Lauren M Popov, Trevor J Parry, Dexter Pratt, Trey Ideker, Nevan J Krogan, Jeffery S Cox

Dynamic post-translational modification profiling of M. tuberculosis-infected primary macrophages

eLife. 2020;9:e51461. doi: 10.7554/eLife.51461 . Datasets assembled into an on-line application: TB OMICS EXPLORER

2019 - Jeng EE, Bhadkamkar V, Ibe NU, Gause H, Jiang L, Chan J, Jian R, Jimenez-Morales D, Stevenson E, Krogan NJ, Swaney DL, Snyder MP, Mukherjee S, Bassik MC.

Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen

Cell Host Microbe.. 2019 Sep 10. pii: S1931-3128(19)30426-3. doi: 10.1016/j.chom.2019.08.017

2019 - Adam L. Orra, Chaeyoung Kima, David Jimenez-Morales, Billy W. Newton, Jeffrey R. Johnson, Nevan J. Krogan, Danielle L. Swaney, and Robert W. Mahley

Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function

Journal of Alzheimer's Disease. 2019;68(3):991-1011. doi: 10.3233/JAD-181184

2018 - L. Bramasole, A. Sinha, S. Gurevich, M. Radzinski, Y. Klein, N. Panat, E. Gefen, T. Rinaldi, D. Jimenez-Morales, J. Johnson, N.J. Krogan, N. Reis, D. Reichmann, M.H. Glickman, E. Pick

Proteasome Lid Bridges Mitochondrial Stress with Cdc53/Cullin1 NEDDylation Status

Redox Biol. 2018 Nov 17; 20:533-543

2018 - Krystal A Fontaine, Kristoffer E Leon, Mir Mubashir Khalid, David Jimenez-Morales, Julia Kaye, Priya Shah, Steven Finkbeiner, Nevan Krogan, Melanie Ott

The cellular NMD pathway restricts Zika virus infection and is targeted by the viral capsid protein

MBio. 2018 Nov 06; 9(6). Pre-printed at bioRxiv.

2018 - Nan Zhao, Vittorio Sebastiano, Natasha Moshkina, Nacho Mena, Judd Hultquist, David Jimenez-Morales, Yixuan Ma, Alexander Rialdi, Randy Albrecht, Romain Fenouil, Maria Teresa Sanchez-Aparicio, Juan Ayllon, Sweta Ravisankar, Bahareh Haddad, Jessica Sook Yuin Ho, Diana Low, Jian Jin, Yurchenko Vyacheslav, Rabinder Prinjha, Alexander Tarakhovsky, Massimo Squatrito, Dalila Pinto, Allette Kimaada, Minji Byun, Melissa Smith, Robert Sebra, Ernesto Guccione, Terrence Tumpey, Nevan Krogan, Harm van Bakel, Benjamin Greenbaum, Adolfo Garcia-Sastre, and Ivan Marazzi

Influenza virus infection causes global RNAPII termination defects

Nature Structural & Molecular Biology. 2018 Sep;25(9):885-893. doi: 10.1038/s41594-018-0124-7. Epub 2018 Sep 3.

2018 - Esther Paulo, Dongmei Wu, Yangmeng Wang, Yun Zhang, Yixuan Wu, Danielle L. Swaney, Margaret Soucheray, David Jimenez-Morales, Ajay Chawla, Nevan J. Krogan & Biao Wang

Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis.

Sci Rep. 2018 Jul 20; 8(1):11001

2018 - Kristin L. Patrick, Jason A. Wojcechowskyj, Tao Jing, Morgan Riba, Sara Talmage, Pengbiao Xu, Samantha L. Bell, Ana L. Cabello, Jiewei Xu, Michael Shales, David Jimenez-Morales, Thomas A. Ficht, Paul de Figueiredo, James E. Samuel1, Pingwei Li, Nevan J. Krogan, Robert O. Watson

Quantitative yeast genetic interaction profiling of bacterial effector proteins uncovers a role for the human retromer in Salmonella infection

Cell Syst. 2018 Jul 26.

2018 - Ruchi Masand, Esther Paulo, Dongmei Wu , Yangmeng Wang, Danielle L. Swaney, David Jimenez-Morales, Nevan J. Krogan, and Biao Wang

Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits.

Cell Metab. 2018 Mar 06; 27(3):616-629.e4

2017 - Rialdi A, Hultquist J, Jimenez-Morales D, Peralta Z, Campisi L, Fenouil R, Moshkina N, Wang Zhen Z, Laffleur B, Michael R, Haas K, Pefanis E, Albrecht A. R, Jen J, Basu U, Garcia-Sastre A, van Bakel H, Krogan N, Marazzi I

The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity.

Cell 2017 May 4;169(4):679-692.e14.

2015 - Basu S, Fey P, Jimenez-Morales D, Dodson RJ, Chisholm RL

dictyBase 2015: Expanding data and annotations in a new software environment.

Genesis 2015 Jun 19.

2014 - Jimenez-Morales D, Adamian L, Shi D, and Liang J.

Lysine Carboxylation: Unveiling a spontaneous posttranslational modification.

Acta Crystallogr D Biol Crystallogr. 2014 Jan;70(Pt 1):48-57

> Supplementary information and PreLysCar.

2012 - Jimenez-Morales D, Liang J, and Eisenberg B.

Ionizable Side Chains at Catalytic Active Sites of Enzymes.

Eur Biophys J. Vol 41, Issue 5 (2012), P 449-460.

2012 - Naveed H, Jimenez-Morales D, Tian J, Pasupuleti V, Kenney L, Liang L (2012).

Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding.

J Mol Biol. 2012 May 25;419(1-2):89-101.

2011 - Liang J, Naveed H, Jimenez-Morales D, Adamian L, Lin M.

Computational studies of membrane proteins: Models and predictions for biological understanding.

Biochim Biophys Acta. 2011 Oct 12.

2011 - Jimenez-Morales D and Liang J.

Pattern of Amino Acid Substitutions in Transmembrane Domains of β-Barrel Membrane Proteins for Detecting Remote Homologs in Bacteria and Mitochondria.

PLoS ONE. 2011;6(11):e26400. Epub 2011 Nov 1.

Supplementary information and bbTM-SearchTool.

2008 - Jimenez-Morales D, Adamian L, and Liang J.

Detecting Remote Homologues Using Scoring Matrices Calculated from the Estimation of Amino Acid Substitution Rates of Beta-Barrel Membrane Proteins.

Conf Proc IEEE Eng Med Biol Soc. 2008, 30:1347-1350.

2008 - Jimenez-Morales D.

Substitution Rates of Amino Acid residues in Transmembrane Regions of Beta-Barrel Membrane Proteins.

BioE Student Journal. N1, 2008. Front Cover.

2001 - Coauthor.

Propiedades adicionales no antibióticas de los macrólidos.

Scientific Communication Management Editors.

2001 - Coauthor.

Guía Setas Autóctonas.

Editorial Doyma. Madrid.

2000 - Jimenez-Morales D.

Problematic in the use of antiobiotics in animal farms.

Nº41. Ganaderos Magazine. sp

2000 - Jimenez-Morales D.

Bovine spongiform encephalopathy.

Nº37. Ganaderos Magazine.

2024 - Jimenez-Morales D, MoTrPAC study group

MoTrPAC Data Hub: Comprehensive Multi-Omic, Multi-Tissue Insights into Exercise Molecular Responses

International Biochemistry of Exercise Conference (IBEC). Limerick, Ireland (July 2024). Oral Communication.

2024 - Jimenez-Morales D, Malene E Lindholm, Jimmy Zhen, Mihir Samdarshi, Jay Yu, Christopher Teng, Archana Raja, David Amar, MoTrPAC study group, Euan A Ashley, Matthew T Wheeler.

MoTrPAC Data Hub: Multi-omic, Multi-tissue Collection of Exercise Molecular Responses

Cell Symposia: Exercise Metabolism. Lisboa, Portugal (May 2024)

2024 - Jimenez-Morales D, MoTrPAC study group

Unveiling the Multi-omic Landscape of Endurance Exercise: Biological Insights and Data Integration from the MoTrPAC Study.

The NIH CFDE All-Hands Meeting. Bethesda, USA (March 2024). Oral Communication, talk awarded.

2021 - Jimenez-Morales D, Raja AN, Hershman SG, Amar D, Petyuk VA, Monroe ME, Nestor MD, Sanford JA, Beltran PMJ, Keshishian H, Mani DR, Ashley EA, Carr SA, Adkins JN, Wheeler MT

CloudProteo: a comprehensive cloud-based proteomics data analysis pipeline

69th Annual Conference American Society for Mass Spectrometry (ASMS) Conference on Mass Spectrometry and Allied Topics. 2021 Philadelphia, Pennsylvania

2021 - Beltran PMJ, Keshishian H, Mundorff C, Pearce C, Mani DR, Karsten Krug, Clauser K, Gay NR, Amar D, Jimenez-Morales D, Sanford JA, Avila Pacheco J, Dennis Courtney, Ilkayeva O, Bodine SC, Gerszten R, Newgard C, Clary Clish C, Carr SA

An Integrative Molecular View of Mammalian Adaptation to Exercise Training

69th Annual Conference American Society for Mass Spectrometry (ASMS) Conference on Mass Spectrometry and Allied Topics. 2021 Philadelphia, Pennsylvania

2019 - David Jimenez-Morales

artMS: Analytical R Tools for Mass Spectrometry (Link to slides)

Oral communication. 2019 SUMS-RAS (Stanford University Mass Spectrometry - Research Application Symposium). Stanford, CA

2019 - David Jimenez-Morales, John Von Dollen, Alexandre Rosa Campos, Nevan J Krogan, Danielle Swaney

artMS: Analytical R Tools for Mass Spectrometry

67th Annual Conference American Society for Mass Spectrometry (ASMS) Conference on Mass Spectrometry and Allied Topicds. 2019 Atlanta, Georgia

2017 - David Jimenez-Morales, Judd Hultquist, John Von Dollen, Jeff Johnson, Hannes Braberg, and Nevan J Krogan

Influenza virus networks of pathogenesis inferred from the integration of multiple large-scale datasets.

Oral communication. Annual Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. May 7-10, 2017 Chicago, IL.

2017 - Kelsey Haas, Michael McGregor, David Jimenez-Morales, Judd Hultquist, and Nevan Krogan

Destroying the “Non-self”: Defining Influenza A Viral Endonuclease Mechanisms for Host Shutoff.

Annual Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. May 7-10, 2017 Chicago, IL.

2017 - Judd F. Hultquist, David Jimenez-Morales, Michael M. McGregor, Kelsey Haas, Jeffrey Johnson, William Newton, Giorgi Metreveli, Matthew Urbanowski, Megan Shaw, Ivan Marazzi, Randy A. Albrecht, Adolfo Garcia-Sastre, and Nevan J. Krogan

Proteomic Profiling of Influenza A Virus Infection Reveals Strain-specific Rewiring of Host Cell Networks.

Annual Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. May 7-10, 2017 Chicago, IL.

2017 - Celina Cahalane, David Jimenez-Morales, John VonDollen, Hannah Baumann, Matthew Urbanowksi, Megan Shaw, Giorgi Metreveli, Nevan Krogan, Adolfo Garcia-Sastre, Oswald Quehenberger, Edward Dennis, and Leah Shriver

Metabolic Profiling of Influenza Infection.

Annual Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. May 7-10, 2017 Chicago, IL.

2016 - David Jimenez-Morales, Judd Hultquist

FluOMICs data integration for the identification of networks involved in host responses to influenza virus infection

Oral communication. The 2016 Systems Biology Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. Apr 10-13, 2016 New York, NY.

2016 - Jimenez-Morales D, Von Dollen J, Braberg H, Verschueren E, and Krogan NJ.

Predictive models for the identification of networks involved in host responses to influenza virus infection.

2nd Annual Host- Pathogen Interactions: Circuits to Systems Symposium. Jan 4, 2016. San Diego, CA.

2015 - Jimenez-Morales D

The new face of dictyBase

Oral communication. dicty2015: Annual International Dictyostelium Conference. August 9th-13th. London, United Kingdom

2011 - Jimenez-Morales D, Liang J, and Eisenberg B.

Active Sites of Enzymes are Crowded with Charge.

Biophysical Journal. 100(3): p. 218a. Abstract 1191-Pos and Poster Board B101.

2011 - Jimenez-Morales D, Liang J, and Eisenberg B.

Active Sites of Enzymes are Crowded with Charge.

6th Annual Midwest Conference on Protein Folding, Assembly, and Molecular Motions. University of Notre Dame.

2010 - Jimenez-Morales D, Li R, Wang Z, Li Y, Liu L, Liang J.

Evolutionary Speed of Enzymes Functional Surfaces and their Relationship with Metabolic Fluxes in Networks of Central Carbon Metabolism of Bacteria.

Biophysical Journal 98(3) pp. 741a

2008 - Jimenez-Morales D, Adamian L, Liang J.

Substitution Rates Of Amino Acid Residues In Transmembrane - Extracellular And Periplasmic- Regions Of Beta-Barrel Membrane Proteins.

Biophysical Journal 94(2) pp. 1959

2002 - Jimenez-Morales D.

Tools for the Apored Virtual.

V-Aporeunión. Tordesillas (Valladolid). Oral presentation: I introduced the improvements in the new Apoweb.

1999 - Jimenez-Morales D, Heredia S, Calvo A, Gomez-Luz ML, Prieto J.

Sensibilidad a antimicrobianos de Enterococcus faecalis de procedencia animal.

Spanish Chemotherapy Society Congress. May 1999

2013 - Jimenez-Morales D

Effects of Physicochemical and Functional Constraints on the Sequence and Structure of Proteins

Bioengineering Department, University of Illinois at Chicago 06/2013